Origin IGS: gataaccagctctacccaaaactttcttgtcttcagcaatcctccaactttagaaagaccttgattaatgccttcagatgagaatggactgactttcttagaatcttgatttataattaaattcgatttaagttagattgttttttatatttttttttgttttctctgtttgtatgcattcgcctttcaaacctttatggttattaagacaaggctgctccaaatgcggtacaaaattacactaattaaatgacataacaaatttttaatactcaaaaatcacttcttaccttgtaattttttacttattctctactttttatcagtaacaggaggagaacaagagcattcaaaggcaaatttgcttatacctttatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taataaaggtataagcaaatttgcctttgaatgctcttgttctcctcctgttactgataaaaagtagagaataagtaaaaaattacaaggtaagaagtgatttttgagtattaaaaatttgttatgtcatttaattagtgtaattttgtaccgcatttggagcagccttgtcttaataaccataaaggtttgaaaggcgaatgcatacaaacagagaaaacaaaaaaaaatataaaaaacaatctaacttaaatcgaatttaattataaatcaagattctaagaaagtcagtccattctcatctgaaggcattaatcaaggtctttctaaagttggaggattgctgaagacaagaaagttttgggtagagctggttatc Mask Tandem Repeat Region ================================================ gataaccagctctacccaaaactttcttgtcttcagcaatcctccaactttagaaagaccttgattaatgccttcagatgagaatggactgactttcttagaatcttgatttataattaaattcgatttaagttagattgttttttatatttttttttgttttctctgtttgtatgcattcgcctttcaaacctttatggttattaagacaaggctgctccaaatgcggtacaaaattacactaattaaatgacataacaaatttttaatactcaaaaatcacttcttaccttgtaattttttacttattctctactttttatcagtaacaggaggagaacaagagcattcaaaggcaaatttgcttatacctttatta Find is-nt database================================================ Query_seq: PI0563:PI0565|PI0563:PI0565:possible integral membrane protein:hypothetical protein:->->:511240..511618 379 gataaccagctctacccaaaactttcttgtcttcagcaatcctccaactttagaaagaccttgattaatgccttcagatgagaatggactgactttcttagaatcttgatttataattaaattcgatttaagttagattgttttttatatttttttttgttttctctgtttgtatgcattcgcctttcaaacctttatggttattaagacaaggctgctccaaatgcggtacaaaattacactaattaaatgacataacaaatttttaatactcaaaaatcacttcttaccttgtaattttttacttattctctactttttatcagtaacaggaggagaacaagagcattcaaaggcaaatttgcttatacctttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0563:PI0565|PI0563:PI0565:possible integral membrane protein:hypothetical protein:->->:511240..511618 379 gataaccagctctacccaaaactttcttgtcttcagcaatcctccaactttagaaagaccttgattaatgccttcagatgagaatggactgactttcttagaatcttgatttataattaaattcgatttaagttagattgttttttatatttttttttgttttctctgtttgtatgcattcgcctttcaaacctttatggttattaagacaaggctgctccaaatgcggtacaaaattacactaattaaatgacataacaaatttttaatactcaaaaatcacttcttaccttgtaattttttacttattctctactttttatcagtaacaggaggagaacaagagcattcaaaggcaaatttgcttatacctttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0563:PI0565|PI0563:PI0565:possible integral membrane protein:hypothetical protein:->->:511240..511618 379 gataaccagctctacccaaaactttcttgtcttcagcaatcctccaactttagaaagaccttgattaatgccttcagatgagaatggactgactttcttagaatcttgatttataattaaattcgatttaagttagattgttttttatatttttttttgttttctctgtttgtatgcattcgcctttcaaacctttatggttattaagacaaggctgctccaaatgcggtacaaaattacactaattaaatgacataacaaatttttaatactcaaaaatcacttcttaccttgtaattttttacttattctctactttttatcagtaacaggaggagaacaagagcattcaaaggcaaatttgcttatacctttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gataaccagctctacccaaaactttcttgtcttcagcaatcctccaactttagaaagaccttgattaatgccttcagatgagaatggactgactttcttagaatcttgatttataattaaattcgatttaagttagattgttttttatatttttttttgttttctctgtttgtatgcattcgcctttcaaacctttatggttattaagacaaggctgctccaaatgcggtacaaaattacactaattaaatgacataacaaatttttaatactcaaaaatcacttcttaccttgtaattttttacttattctctactttttatcagtaacaggaggagaacaagagcattcaaaggcaaatttgcttatacctttatta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 138 End: 242 ......................................................................................................................................... M F F I F F F V F S V C M H S P F K P L W L L R Q G C S K C G T K L H ......................................................................................................................................... Protein_Len: 38 Strand: + Start: 137 End: 250 ........................................................................................................................................ M V F Y I F F C F L C L Y A F A F Q T F M V I K T R L L Q M R Y K I T L I K ................................................................................................................................. Protein_Len: 37 Strand: + Start: 269 End: 379 ............................................................................................................................................................................................................................................................................ M L K N H F L P C N F L L I L Y F L S V T G G E Q E H S K A N L L I P L L Protein_Len: 31 Strand: - Start: 131 End: 223 .................................................................................................................................. T L N N K I N K K T K E T Q I C E G K L G K H N N L C P Q E M ............................................................................................................................................................ Protein_Len: 39 Strand: - Start: 1 End: 117 I V L E V W F K R T K L L G G V K S L G Q N I G E S S F P S V K K S D Q N I M ...................................................................................................................................................................................................................................................................... gataaccagctctacccaaaactttcttgtcttcagcaatcctccaactttagaaagaccttgattaatgccttcagatgagaatggactgactttcttagaatcttgatttataattaaattcgatttaagttagattgttttttatatttttttttgttttctctgtttgtatgcattcgcctttcaaacctttatggttattaagacaaggctgctccaaatgcggtacaaaattacactaattaaatgacataacaaatttttaatactcaaaaatcacttcttaccttgtaattttttacttattctctactttttatcagtaacaggaggagaacaagagcattcaaaggcaaatttgcttatacctttatta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 88 End: 117 .......................................................................................ACTGACTTTCTTAGAATCTTGATTTATAAT...................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gataaccagctctacccaaaactttcttgtcttcagcaatcctccaactttagaaagaccttgattaatgccttcagatgagaatggactgactttcttagaatcttgatttataattaaattcgatttaagttagattgttttttatatttttttttgttttctctgtttgtatgcattcgcctttcaaacctttatggttattaagacaaggctgctccaaatgcggtacaaaattacactaattaaatgacataacaaatttttaatactcaaaaatcacttcttaccttgtaattttttacttattctctactttttatcagtaacaggaggagaacaagagcattcaaaggcaaatttgcttatacctttatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -2.3 Tail_Score: -5.72118 Start: 124 End: 140 Full_Region: ATTTATAATTAAATT CGATTTA AGT TAGATTG TTTTTTATATTTTTT ...........................................................................................................................CGATTTAAGTTAGATTG............................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 78 HP_score: -4.0 Tail_Score: -5.39221 Start: 287 End: 297 Full_Region: CTCAAAAATCACTTC TTAC CTT GTAA TTTTTTACTTATTCT ..............................................................................................................................................................................................................................................................................................TTACCTTGTAA.................................................................................. Find igs database================================================ Query_seq: PI0563:PI0565|PI0563:PI0565:possible integral membrane protein:hypothetical protein:->->:511240..511618 379 gataaccagctctacccaaaactttcttgtcttcagcaatcctccaactttagaaagaccttgattaatgccttcagatgagaatggactgactttcttagaatcttgatttataattaaattcgatttaagttagattgttttttatatttttttttgttttctctgtttgtatgcattcgcctttcaaacctttatggttattaagacaaggctgctccaaatgcggtacaaaattacactaattaaatgacataacaaatttttaatactcaaaaatcacttcttaccttgtaattttttacttattctctactttttatcagtaacaggaggagaacaagagcattcaaaggcaaatttgcttatacctttatta Intra-Species Hit: Count: 1 Min: 1 Max: 379 Len: 379 Subject: pint_PI0563_PI0565|possible integral membrane protein:hypothetical protein|POSITIVE:POSITIVE|[511240,511618]|379 HSP 1 e-value: 1.0E-119 bit: 428.0 Len: 216 Query Start:164 Query End:379 Subject Strand: POSITIVE Subject Start: 164 Subject End: 379 ...................................................................................................................................................................ctctgtttgtatgcattcgcctttcaaacctttatggttattaagacaaggctgctccaaatgcggtacaaaattacactaattaaatgacataacaaatttttaatactcaaaaatcacttcttaccttgtaattttttacttattctctactttttatcagtaacaggaggagaacaagagcattcaaaggcaaatttgcttatacctttatta ...................................................................................................................................................................ctctgtttgtatgcattcgcctttcaaacctttatggttattaagacaaggctgctccaaatgcggtacaaaattacactaattaaatgacataacaaatttttaatactcaaaaatcacttcttaccttgtaattttttacttattctctactttttatcagtaacaggaggagaacaagagcattcaaaggcaaatttgcttatacctttatta HSP 2 e-value: 1.0E-73 bit: 278.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 gataaccagctctacccaaaactttcttgtcttcagcaatcctccaactttagaaagaccttgattaatgccttcagatgagaatggactgactttcttagaatcttgatttataattaaattcgatttaagttagattg............................................................................................................................................................................................................................................... gataaccagctctacccaaaactttcttgtcttcagcaatcctccaactttagaaagaccttgattaatgccttcagatgagaatggactgactttcttagaatcttgatttataattaaattcgatttaagttagattg............................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAACCAGCUCUACCCAAAACUUUCUUGUCUUCAGCAAUCCUCCAACUUUAGAAAGACCUUGAUUAAUGCCUUCAGAUGAGAAUGGACUGACUUUCUUAGAAUCUUGAUUUAUAAUUAAAUUCGAUUUAAGUUAGAUUGUUUUUUAUAUUUUUUUUUGUUUUCUCUGUUUGUAUGCAUUCGCCUUUCAAACCUUUAUGGUUAUUAAGACAAGGCUGCUCCAAAUGCGGUACAAAAUUACACUAAUUAAAUGACAUAACAAAUUUUUAAUACUCAAAAAUCACUUCUUACCUUGUAAUUUUUUACUUAUUCUCUACUUUUUAUCAGUAACAGGAGGAGAACAAGAGCAUUCAAAGGCAAAUUUGCUUAUACCUUUAUUA (((((...(((((............((((((((...................(((((.(..((....((((...((((.(((((..(((((((((.....((((.(((((.....))))))))).....)))))))..(((.....)))......))..)))))))))...)))).))...).))))).((((.....))))...)))))))).((.((((......((((.(((((((((.........((......)).((((((.......))))))............))))))))).)))).......((((.......))))...)))).))....)))))......(((((....)))))......))))). (-66.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAAGGUAUAAGCAAAUUUGCCUUUGAAUGCUCUUGUUCUCCUCCUGUUACUGAUAAAAAGUAGAGAAUAAGUAAAAAAUUACAAGGUAAGAAGUGAUUUUUGAGUAUUAAAAAUUUGUUAUGUCAUUUAAUUAGUGUAAUUUUGUACCGCAUUUGGAGCAGCCUUGUCUUAAUAACCAUAAAGGUUUGAAAGGCGAAUGCAUACAAACAGAGAAAACAAAAAAAAAUAUAAAAAACAAUCUAACUUAAAUCGAAUUUAAUUAUAAAUCAAGAUUCUAAGAAAGUCAGUCCAUUCUCAUCUGAAGGCAUUAAUCAAGGUCUUUCUAAAGUUGGAGGAUUGCUGAAGACAAGAAAGUUUUGGGUAGAGCUGGUUAUC .......((((..(((...((((.(((..(((((.(((((((((.......((((.......)))))))))))))...(((((((((.......(((((((...(((((.......)))))....)))))))......))))))))).....)))))..)))..((.(((((((...((((.....))))...)))))))..)).......))))...............(((..(((((..(((..((((((((..(((((....)))))...)))).))))...(((.(.((.(((......)))))).....(((.((((((((.......))))))))..))).))).)))..)))))..)))..)))...)))) (-76.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 90 42 67 29 pint:PI1045|5end_cytidine/deoxycytidylate_deaminase_family_protein_965104..965334_POSITIVE 313 184 141 75 26 pint:PI0173|5end_hypothetical_protein_165305..165535_POSITIVE 309 218 172 88 35 pint:PI0870|5end_branched-chain_amino_acid_aminotransferase_805933..806163_POSITIVE 288 367 325 126 86 pint:PI1199|5end_possible_acetyltransferase_1115139..1115369_POSITIVE 281 229 191 44 6 pint:PI1506|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_(queuine_synthetase)_1425370..1425600_POSITIVE 272 225 181 191 149 pint:PI0674|5end_conserved_hypothetical_protein_613711..613941_POSITIVE 272 225 181 127 85 pint:PI0675|5end_hypothetical_protein_613647..613877_POSITIVE 272 220 176 213 159 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 270 229 181 175 141 pint:PI1659|5end_hypothetical_protein_1574725..1574955_POSITIVE 270 229 181 109 75 pint:PI1660|5end_hypothetical_protein_1574659..1574889_POSITIVE 268 229 182 228 181 pint:PI0333|5end_hypothetical_protein_313478..313708_POSITIVE 264 45 5 156 112 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 259 227 181 231 174 pint:PI1335|5end_Fe-S_oxidoreductase_1252818..1253048_POSITIVE 259 34 8 178 150 pint:PI1121|5end_glycosyltransferase_1045995..1046225_POSITIVE 259 231 197 56 3 pint:PI0610|5end_conserved_hypothetical_protein_557403..557633_POSITIVE 258 229 184 60 21 pint:PI1001|5end_hypothetical_protein_923510..923740_POSITIVE 258 200 165 159 120 pint:PI0959|5end_uridine_kinase_890495..890725_POSITIVE 258 200 157 201 149 pint:PI0463|5end_50S_ribosomal_protein_L2_434158..434388_POSITIVE 256 94 56 71 30 pint:PI0160|5end_conserved_hypothetical_protein_152610..152840_POSITIVE 255 360 318 132 84 pint:PI0178|5end_2-oxoglutarate_synthase,_subunit_korA_169524..169754_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 230 181 123 84 pint:PI0646|3end_hypothetical_protein_587205..587355_POSITIVE 288 367 325 126 86 pint:PI1198|3end_acetyltransferase_1115219..1115369_POSITIVE 270 229 181 106 72 pint:PI1658|3end_conserved_hypothetical_protein_1574736..1574886_POSITIVE 266 47 7 132 91 pint:PI0745|3end_conserved_hypothetical_protein_675670..675820_POSITIVE 258 229 184 142 103 pint:PI1000|3end_conserved_hypothetical_protein_923672..923822_POSITIVE 255 230 182 147 101 pint:PI1260|3end_IS1001-related_transposase_1183272..1183422_POSITIVE 255 233 195 132 89 pint:PI0516|3end_ferredoxin,_4Fe-4S_476108..476258_POSITIVE 255 360 318 111 63 pint:PI0177|3end_2-oxoglutarate_synthase,_subunit_korB_169583..169733_POSITIVE 254 229 181 130 77 pint:PI0890|3end_ribose_5-phosphate_isomerase_B_820931..821081_POSITIVE 251 89 51 147 107 pint:PI0263|3end_conjugative_transposon_protein,_TraM_256412..256562_POSITIVE 250 200 151 76 30 pint:PI1786|3end_hypothetical_protein_1718380..1718530_POSITIVE 249 60 18 55 23 pint:PI0218|3end_conserved_hypothetical_protein_211149..211299_POSITIVE 245 219 176 60 9 pint:PI2161|3end_hypothetical_protein_2108751..2108901_POSITIVE 244 319 273 54 13 pint:PI0926|3end_hypothetical_protein_857047..857197_POSITIVE 243 47 6 135 92 pint:PI0380|3end_conserved_hypothetical_protein_350541..350691_POSITIVE 242 218 175 111 52 pint:PI1599|3end_predicted_TPR-repeat-containing_protein_1529176..1529326_POSITIVE 241 198 165 150 114 pint:PI0958|3end_G:T/U_mismatch-specific_DNA_glycosylase_890569..890719_POSITIVE 240 195 157 102 57 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE 236 233 195 138 99 pint:PI0855|3end_hypothetical_protein_789545..789695_POSITIVE 235 45 5 130 94 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE